Showing papers by "Pacific Northwest National Laboratory published in 2003"

Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer.

Abstract: The potential for removing uranium from contaminated groundwater by stimulating the in situ activity of dissimilatory metal-reducing microorganisms was evaluated in a uranium-contaminated aquifer located in Rifle, Colo. Acetate (1 to 3 mM) was injected into the subsurface over a 3-month period via an injection gallery composed of 20 injection wells, which was installed upgradient from a series of 15 monitoring wells. U(VI) concentrations decreased in as little as 9 days after acetate injection was initiated, and within 50 days uranium had declined below the prescribed treatment level of 0.18 μM in some of the monitoring wells. Analysis of 16S ribosomal DNA (rDNA) sequences and phospholipid fatty acid profiles demonstrated that the initial loss of uranium from the groundwater was associated with an enrichment of Geobacter species in the treatment zone. Fe(II) in the groundwater also increased during this period, suggesting that U(VI) reduction was coincident with Fe(III) reduction. As the acetate injection continued over 50 days there was a loss of sulfate from the groundwater and an accumulation of sulfide and the composition of the microbial community changed. Organisms with 16S rDNA sequences most closely related to those of sulfate reducers became predominant, and Geobacter species became a minor component of the community. This apparent switch from Fe(III) reduction to sulfate reduction as the terminal electron accepting process for the oxidation of the injected acetate was associated with an increase in uranium concentration in the groundwater. These results demonstrate that in situ bioremediation of uranium-contaminated groundwater is feasible but suggest that the strategy should be optimized to better maintain long-term activity of Geobacter species.

Flow-cytometric isolation of human antibodies from a nonimmune Saccharomyces cerevisiae surface display library

Abstract: A nonimmune library of 10(9) human antibody scFv fragments has been cloned and expressed on the surface of yeast, and nanomolar-affinity scFvs routinely obtained by magnetic bead screening and flow-cytometric sorting. The yeast library can be amplified 10(10)-fold without measurable loss of clonal diversity, allowing its effectively indefinite expansion. The expression, stability, and antigen-binding properties of >50 isolated scFv clones were assessed directly on the yeast cell surface by immunofluorescent labeling and flow cytometry, obviating separate subcloning, expression, and purification steps and thereby expediting the isolation of novel affinity reagents. The ability to use multiplex library screening demonstrates the usefulness of this approach for high-throughput antibody isolation for proteomics applications.

Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs

Abstract: The Crp-Fnr regulators, named after the first two identified members, are DNA-binding proteins which predominantly function as positive transcription factors, though roles of repressors are also important. Among over 1200 proteins with an N-terminally located nucleotide-binding domain similar to the cyclic adenosine monophosphate (cAMP) receptor protein, the distinctive additional trait of the Crp-Fnr superfamily is a C-terminally located helix-turn-helix motif for DNA binding. From a curated database of 369 family members exhibiting both features, we provide a protein tree of Crp-Fnr proteins according to their phylogenetic relationships. This results in the assembly of the regulators ArcR, CooA, CprK, Crp, Dnr, FixK, Flp, Fnr, FnrN, MalR, NnrR, NtcA, PrfA, and YeiL and their homologs in distinct clusters. Lead members and representatives of these groups are described, placing emphasis on the less well-known regulators and target processes. Several more groups consist of sequence-derived proteins of unknown physiological roles; some of them are tight clusters of highly similar members. The Crp-Fnr regulators stand out in responding to a broad spectrum of intracellular and exogenous signals such as cAMP, anoxia, the redox state, oxidative and nitrosative stress, nitric oxide, carbon monoxide, 2-oxoglutarate, or temperature. To accomplish their roles, Crp-Fnr members have intrinsic sensory modules allowing the binding of allosteric effector molecules, or have prosthetic groups for the interaction with the signal. The regulatory adaptability and structural flexibility represented in the Crp-Fnr scaffold has led to the evolution of an important group of physiologically versatile transcription factors.

Selection and Evaluation of Heat-Resistant Alloys for SOFC Interconnect Applications

Abstract: Over the past several years, the steady reduction in SOFC operating temperatures to the intermediate range of 700~850oC [1] has made it feasible for lanthanum chromite to be supplanted by metals or alloys as the interconnect materials. Compared to doped lanthanum chromite, metals or alloys offer significantly lower raw material and fabrication costs. However, to be a durable and reliable, a metal or alloy has to satisfy several functional requirements specific to the interconnect under SOFC operating conditions. Specifically, the interconnect metal or alloy should possess the following properties: (i) Good surface stability (resistance to oxidation, hot corrosion, and carburization) in both cathodic (air) and anodic (fuel) atmospheres; (ii) Thermal expansion matching to the ceramic PEN (positive cathode-electrolyte-negative anode) and seal materials (as least for a rigid seal design); (iii) High electrical conductivity through both the bulk material and in-situ formed oxide scales; (iv) Bulk and interfacial thermal mechanical reliability and durability at the operating temperature; (v) Compatibility with other materials in contact with interconnects such as seals and electrical contact materials.

U.S. Agriculture and Climate Change: New Results

Abstract: We examined the impacts on U.S. agriculture of transient climate change as simulated by 2 global general circulation models focusing on the decades of the 2030s and 2090s. We examined historical shifts in the location of crops and trends in the variability of U.S. average crop yields, finding that non-climatic forces have likely dominated the north and westward movement of crops and the trends in yield variability. For the simulated future climates we considered impacts on crops, grazing and pasture, livestock, pesticide use, irrigation water supply and demand, and the sensitivity to international trade assumptions, finding that the aggregate of these effects were positive for the U.S. consumer but negative, due to declining crop prices, for producers. We examined the effects of potential changes in El Nino/Southern Oscillation (ENSO) and impacts on yield variability of changes in mean climate conditions. Increased losses occurred with ENSO intensity and frequency increases that could not be completely offset even if the events could be perfectly forecasted. Effects on yield variability of changes in mean temperatures were mixed. We also considered case study interactions of climate, agriculture, and the environment focusing on climate effects on nutrient loading to the Chesapeake Bay and groundwater depletion of the Edward's Aquifer that provides water for municipalities and agriculture to the San Antonio, Texas area. While only case studies, these results suggest environmental targets such as pumping limits and changes in farm practices to limit nutrient run-off would need to be tightened if current environmental goals were to be achieved under the climate scenarios we examined

Cell and organ printing 2: Fusion of cell aggregates in three‐dimensional gels

Abstract: We recently developed a cell printer (Wilson and Boland, 2003) that enables us to place cells in positions that mimic their respective positions in organs. However, this technology was limited to the printing of two-dimensional (2D) tissue constructs. Here we describe the use of thermosensitive gels to generate sequential layers for cell printing. The ability to drop cells on previously printed successive layers provides a real opportunity for the realization of three-dimensional (3D) organ printing. Organ printing will allow us to print complex 3D organs with computer-controlled, exact placing of different cell types, by a process that can be completed in several minutes. To demonstrate the feasibility of this novel technology, we showed that cell aggregates can be placed in the sequential layers of 3D gels close enough for fusion to occur. We estimated the optimum minimal thickness of the gel that can be reproducibly generated by dropping the liquid at room temperature onto a heated substrate. Then we generated cell aggregates with the corresponding (to the minimal thickness of the gel) size to ensure a direct contact between printed cell aggregates during sequential printing cycles. Finally, we demonstrated that these closely-placed cell aggregates could fuse in two types of thermosensitive 3D gels. Taken together, these data strongly support the feasibility of the proposed novel organ-printing technology. Anat Rec Part A 272A:497–502, 2003. © 2003 Wiley-Liss, Inc.

Monthly averages of aerosol properties: A global comparison among models, satellite data, and AERONET ground data

Abstract: [1] New aerosol modules of global (circulation and chemical transport) models are evaluated. These new modules distinguish among at least five aerosol components: sulfate, organic carbon, black carbon, sea salt, and dust. Monthly and regionally averaged predictions for aerosol mass and aerosol optical depth are compared. Differences among models are significant for all aerosol types. The largest differences were found near expected source regions of biomass burning (carbon) and dust. Assumptions for the permitted water uptake also contribute to optical depth differences (of sulfate, organic carbon, and sea salt) at higher latitudes. The decline of mass or optical depth away from recognized sources reveals strong differences in aerosol transport or removal among models. These differences are also a function of altitude, as transport biases of dust do not always extend to other aerosol types. Ratios of optical depth and mass demonstrate large differences in the mass extinction efficiency, even for hydrophobic aerosol. This suggests that efforts of good mass simulations could be wasted or that conversions are misused to cover for poor mass simulations. In an attempt to provide an absolute measure for model skill, simulated total optical depths (when adding contributions from all five aerosol types) are compared to measurements from ground and space. Comparisons to the Aerosol Robotic Network (AERONET) suggest a source strength underestimate in many models, most frequently for (subtropical) tropical biomass or dust. Comparisons to the combined best of Moderate-Resolution Imaging Spectroradiometer (MODIS) and Total Ozone Mapping Spectrometer (TOMS) indicate that away from sources, model simulations are usually smaller. Particularly large are discrepancies over tropical oceans and oceans of the Southern Hemisphere, raising issues on the treatment of sea salt in models. Totals for mass or optical depth in many models are defined by the absence or dominance of only one aerosol component. With appropriate corrections to that component (e.g., to removal, to source strength, or to seasonality) a much better model performance can be expected. Still, many important modeling issues remain inconclusive as the combined result of poor coordination (different emissions and meteorology), insufficient model output (vertical distributions, water uptake by aerosol type), and unresolved measurement issues (retrieval assumptions and temporal or spatial sampling biases).

An ab initio model of electron transport in hematite (α-Fe2O3) basal planes

Abstract: Transport of conduction electrons through basal planes of the hematite lattice was modeled as a valence alternation of iron cations using ab initio molecular orbital calculations and electron transfer theory. A cluster approach was successfully implemented to compute electron-transfer rate-controlling quantities such as the reorganization energy and electronic coupling matrix element. Localization of a conduction electron at an iron lattice site is accompanied by large iron–oxygen bond length increases that give rise to a large internal component of the reorganization energy (1.03 eV). The internal reorganization energy calculated directly is shown to differ from Nelsen’s four-point method due to the short-range covalent bridge interaction between the Fe–Fe electron transfer pair in the hematite structure. The external reorganization energy arising from modification of the lattice polarization surrounding the localization site is predicted to contribute significantly to the total reorganization energy. Th...

Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses.

Abstract: The use of artificial neural networks (ANNs) is described for predicting the reversed-phase liquid chromatography retention times of peptides enzymatically digested from proteome-wide proteins. To enable the accurate comparison of the numerous LC/MS data sets, a genetic algorithm was developed to normalize the peptide retention data into a range (from 0 to 1), improving the peptide elution time reproducibility to ∼1%. The network developed in this study was based on amino acid residue composition and consists of 20 input nodes, 2 hidden nodes, and 1 output node. A data set of ∼7000 confidently identified peptides from the microorganism Deinococcus radiodurans was used for the training of the ANN. The ANN was then used to predict the elution times for another set of 5200 peptides tentatively identified by MS/MS from a different microorganism (Shewanella oneidensis). The model was found to predict the elution times of peptides with up to 54 amino acid residues (the longest peptide identified after tryptic d...

Inhibition of bacterial U(VI) reduction by calcium

Abstract: The rapid kinetics of bacterial U(VI) reduction and low solubility of uraninite (UO2,cr) make this process an attractive option for removing uranium from groundwater Nevertheless, conditions that may promote or inhibit U(VI) reduction are not well-defined Recent descriptions of Ca-UO2-CO3 complexes indicate that these species may dominate the aqueous speciation of U(VI) in many environments We monitored the bacterial reduction of U(VI) in bicarbonate-buffered solution in the presence and absence of Ca XAFS measurements confirmed the presence of a Ca-U(VI)-CO3 complex in the initial solutions containing calcium Calcium, at millimolar concentrations (045-5 mM), caused a significant decrease in the rate and extent of bacterial U(VI) reduction Both facultative (Shewanella putrefaciens strain CN32) and obligate (Desulfovibrio desulfuricans, Geobacter sulfurreducens) anaerobic bacteria were affected by the presence of calcium Reduction of U(VI) ceased when the calculated system Eh re ached -0046+/- 0001 V, based on the Ca2UO2(CO3)(3) --> UO2,cr couple The results are consistent with the hypothesis that U is a less energetically favorable electron acceptor when the Ca-UO2-CO3 complexes are present The results do not support Ca inhibition caused by direct interactions with the cells or with the electron donor as the reduction of fumarate or Tc(VII)O-4(-) under identical conditions wasmore » unaffected by the presence of Ca« less

Single-Enzyme Nanoparticles Armored by a Nanometer-Scale Organic/Inorganic Network

Abstract: We have developed armored single-enzyme nanoparticles (SENs) that surround each enzyme molecule with a porous composite organic/inorganic network of less than a few nanometers thick. This approach ...

Radiation Effects in Zircon

Abstract: The widespread distribution of zircon in the continental crust, its tendency to concentrate trace elements, particularly lanthanides and actinides, its use in age-dating, and its resistance to chemical and physical degradation have made zircon the most important accessory mineral in geologic studies. Because zircon is highly refractory, it also has important industrial applications, including its use as a lining material in high-temperature furnaces. However, during the past decade, zircon has also been proposed for advanced technology applications, such as a durable material for the immobilization of plutonium or, when modified by ion-beam irradiation, as an optic waveguide material. In all of these applications, the change in properties as a function of increasing radiation dose is of critical importance. In this chapter, we summarize the state-of-knowledge on the radiation damage accumulation process in zircon.

Dry Bias and Variability in Vaisala RS80-H Radiosondes: The ARM Experience

Abstract: Thousands of comparisons between total precipitable water vapor (PWV) obtained from radiosonde (Vaisala RS80-H) profiles and PWV retrieved from a collocated microwave radiometer (MWR) were made at the Atmospheric Radiation Measurement (ARM) Program’s Southern Great Plains Cloud and Radiation Testbed (SGP CART) site in northern Oklahoma from 1994 to 2000. These comparisons show that the RS80-H radiosonde has an approximate 5% dry bias compared to the MWR. This observation is consistent with interpretations of Vaisala RS80 radiosonde data obtained during the Tropical Ocean Global Atmosphere Coupled Ocean‐Atmosphere Response Experiment (TOGA COARE). In addition to the dry bias, analysis of the PWV comparisons as well as of data obtained from dual-sonde soundings done at the SGP show that the calibration of the radiosonde humidity measurements varies considerably both when the radiosondes come from different calibration batches and when the radiosondes come from the same calibration batch. This variability can result in peak-to-peak differences between radiosondes of greater than 25% in PWV. Because accurate representation of the vertical profile of water vapor is critical for ARM’s science objectives, an empirical method for correcting the radiosonde humidity profiles is developed based on a constant scaling factor. By using an independent set of observations and radiative transfer models to test the correction, it is shown that the constant humidity scaling method appears both to improve the accuracy and reduce the uncertainty of the radiosonde data. The ARM data are also used to examine a different, physically based, correction scheme that was developed recently by scientists from Vaisala and the National Center for Atmospheric Research (NCAR). This scheme, which addresses the dry bias problem as well as other calibration-related problems with the RS80-H sensor, results in excellent agreement between the PWV retrieved from the MWR and integrated from the corrected radiosonde. However, because the physically based correction scheme does not address the apparently random calibration variations observed, it does not reduce the variability either between radiosonde calibration batches or within individual calibration batches.

Cloud Coverage Based on All-Sky Imaging and Its Impact on Surface Solar Irradiance

Abstract: In Lauder, Central Otago, New Zealand, two all-sky imaging systems have been in operation for more than 1 yr, measuring the total, opaque, and thin cloud fraction, as well as indicating whether the sun is obscured by clouds. The data provide a basis for investigating the impact of clouds on the surface radiation field. The allsky cloud parameters were combined with measurements of global, direct, and diffuse surface solar irradiance over the spectral interval from 0.3 to 3 mm. Here, the results of ongoing analysis of this dataset are described. As a reference for the magnitude of the cloud influence, clear-sky irradiance values are estimated as a simple function of solar zenith angle and the earth‐sun distance. The function is derived from a least squares fit to measurements taken when available cloud images show clear-sky situations. Averaged over a longer time period, such as 1 month, cloud fraction and surface irradiance are clearly negatively correlated. Monthly means in the ratio of the measured surface irradiance to the clear-sky value had a correlation coefficient of about 20.9 with means of cloud fraction for the months from July 2000 to June 2001. In the present work reductions in the surface irradiance and situations in which clouds cause radiation values to exceed the expected clear-sky amount are analyzed. Over 1 yr of observations, 1-min-averaged radiation measurements exceeding the expected clearsky value by more than 10% were observed with a frequency of 5%. In contrast, a reduction of more than 10% below estimated clear-sky values occurred in 66% of the cases, while clear-sky irradiances (measured irradiance within 610% of estimated clear-sky value) were observed 29% of the time. Low cloud fractions frequently lead to moderate enhancement, because the sun is often unobscured and the clouds are brighter than the sky that they hide. As cloud fraction increases the sun is likely to be obscured, causing irradiance values to fall well below clear-sky values. However, in the case of unobscured sun, there is a tendency for strongest enhancements when cloud fractions are highest. Enhancements, especially at high solar zenith angle, are also often observed in association with thin clouds.

Reactions at Interfaces As a Source of Sulfate Formation in Sea-Salt Particles

Abstract: Understanding the formation of sulfate particles in the troposphere is critical because of their health effects and their direct and indirect effects on radiative forcing, and hence on climate. Laboratory studies of the chemical and physical changes in sodium chloride, the major component of sea-salt particles, show that sodium hydroxide is generated upon reaction of deliquesced sodium chloride particles with gas-phase hydroxide. The increase in alkalinity will lead to an increase in the uptake and oxidation of sulfur dioxide to sulfate in sea-salt particles. This chemistry is missing from current models but is consistent with a number of previously unexplained field study observations.

Dynamic π−π Stacked Molecular Assemblies Emit from Green to Red Colors

Abstract: We present a dynamic molecular self-assembly system, driven mostly by π−π molecular orbital interactions. The formation of such self-organized dynamic systems is characterized with absorption, fluorescence, and NMR spectroscopies as well as dynamic light scattering. Our results demonstrate that proper design of molecules can promote self-organization in solution. As a result, we observed distinct red, orange, yellow, and green photoluminescence from different initial concentrations while exciting the system at the same wavelength.

[Ni(Et2PCH2NMeCH2PEt2)2]2+ as a Functional Model for Hydrogenases

Abstract: The reaction of Et2PCH2N(Me)CH2PEt2 (PNP) with [Ni(CH3CN)6](BF4)2 results in the formation of [Ni(PNP)2](BF4)2, which possesses both hydride- and proton-acceptor sites. This complex is an electrocatalyst for the oxidation of hydrogen to protons, and stoichiometric reaction with hydrogen forms [HNi(PNP)(PNHP)](BF4)2, in which a hydride ligand is bound to Ni and a proton is bound to a pendant N atom of one PNP ligand. The free energy associated with this reaction has been calculated to be −5 kcal/mol using a thermodynamic cycle. The hydride ligand and the NH proton undergo rapid intramolecular exchange with each other and intermolecular exchange with protons in solution. [HNi(PNP)(PNHP)](BF4)2 undergoes reversible deprotonation to form [HNi(PNP)2](BF4) in acetonitrile solutions (pKa = 10.6). A convenient synthetic route to the PF6- salt of this hydride involves the reaction of PNP with Ni(COD)2 to form Ni(PNP)2, followed by protonation with NH4PF6. A pKa of value of 22.2 was measured for this hydride. This ...

The Cement Industry and Global Climate Change: Current and Potential Future Cement Industry CO2 Emissions

Abstract: Publisher Summary The cement industry is responsible for approximately 5% of global anthropogenic carbon dioxide emissions Atmospheric concentrations of greenhouse gases cannot be stabilized without addressing this important emissions source The industry emits nearly 900 kg of CO2 for every 1000 kg of cement produced As a result of the significant emissions per unit of cement produced, emerging climate change policies have the potential to place the industry at significant financial risk To create the foundation for an industry-wide climate change response strategy and manage the associated environmental and financial risk, ten of the world's largest cement companies, under the auspices of the World Business Council for Sustainable Development, sponsored a quantitative assessment of current and potential future CO2 emissions from the cement industry in 14 regions of the world Quantitatively, current and potential future cement industry greenhouse gas emissions are evaluated under the new family of Intergovernmental Panel on Climate Change (IPCC) scenarios that were developed as part of the Third Assessment and documented in the Special Report on Emissions Scenarios (SRES) The results of the assessment show that if the industry does not improve its current specific emissions, its relative contribution to anthropogenic CO2 emissions would increase by more than one order of magnitude over the next century The industry faces several challenges as it seeks to reduce its specific CO2 emissions, including its heavy dependence on fossil fuels (especially high-carbon fossil fuels), its dependence on limestone-based clinker, and the age and efficiency of its capital stock, especially in regions where future demand is expected to be high

Mutual disambiguation of 3D multimodal interaction in augmented and virtual reality

Abstract: We describe an approach to 3D multimodal interaction in immersive augmented and virtual reality environments that accounts for the uncertain nature of the information sources. The resulting multimodal system fuses symbolic and statistical information from a set of 3D gesture, spoken language, and referential agents. The referential agents employ visible or invisible volumes that can be attached to 3D trackers in the environment, and which use a time-stamped history of the objects that intersect them to derive statistics for ranking potential referents. We discuss the means by which the system supports mutual disambiguation of these modalities and information sources, and show through a user study how mutual disambiguation accounts for over 45% of the successful 3D multimodal interpretations. An accompanying video demonstrates the system in action.

Templateless Assembly of Molecularly Aligned Conductive Polymer Nanowires: A New Approach for Oriented Nanostructures

Abstract: Although oriented carbon nanotubes, oriented nanowires of metals, semiconductors and oxides have attracted wide attention, there have been few reports on oriented polymer nanostructures such as nanowires In this paper we report the assembly of large arrays of oriented nanowires containing molecularly aligned conducting polymers (polyaniline) without using a porous membrane template to support the polymer The uniform oriented nanowires were prepared through controlled nucleation and growth during a stepwise electrochemical deposition process in which a large number of nuclei were first deposited on the substrate using a large current density After the initial nucleation, the current density was reduced stepwise in order to grow the oriented nanowires from the nucleation sites created in the first step The usefulness of these new polymer structures is demonstrated with a chemical sensor device for H(2)O(2), the detection of which is widely investigated for biosensors Finally, we demonstrated that controlled nucleation and growth is a general approach and has potential for growing oriented nanostructures of other materials

Cold Air Pool Structure and Evolution in a Mountain Basin: Peter Sinks, Utah

Abstract: The evolution of potential temperature and wind structure during the buildup of nocturnal cold-air pools was investigated during clear, dry, September nights in Utah's Peter Sinks basin, a 1-km-diameter limestone sinkhole that holds the Utah minimum temperature record of −56°C. The evolution of cold-pool characteristics depended on the strength of prevailing flows above the basin. On an undisturbed day, a 30°C diurnal temperature range and a strong nocturnal potential temperature inversion (22 K in 100 m) were observed in the basin. Initially, downslope flows formed on the basin sidewalls. As a very strong potential temperature jump (17 K) developed at the top of the cold pool, however, the winds died within the basin and over the sidewalls. A persistent turbulent sublayer formed below the jump. Turbulent sensible heat flux on the basin floor became negligible shortly after sunset while the basin atmosphere continued to cool. Temperatures over the slopes, except for a 1–2-m-deep layer, became war...

Supercritical Fluid Fabrication of Metal Nanowires and Nanorods Templated by Multiwalled Carbon Nanotubes

Abstract: A rapid, direct and clean approach has been developed to synthesize metal (Pd, Ni and Cu) nanowires and nanorods using multi-walled carbon nanotubes (MWCNTs) as templates and supercritical CO{sub 2} as the reaction medium. Filling of metals into MWCNTs to form nanowires or nanorods was easily achieved by the simple hydrogen reduction of metal-b-diketone complexes in supercritical CO{sub 2}.